Analysis of Antimicrobial Minimum Inhibitory Concentration Data

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Documentation for package ‘MIC’ version 1.0.2

• DESCRIPTION file.
• Package NEWS.

Help Pages

bias	Calculate MIC bias
clean_raw_mic	Clean up raw MIC for use as a feature
combined_file_system	Combine train and test filesystem into single folder
compare_mic	Compare and validate MIC values
compare_sir	Compare SIR results and generate categorical agreement
download_patric_db	Download PATRIC database
ecoffs	ECOFF data
essential_agreement	Essential agreement for MIC validation
example_mics	Example MIC data
fill_dilution_levels	Fill MIC dilution levels
force_mic	Force MIC-like into MIC-compatible format
genomes_to_kmer_libsvm	Convert genomes to kmers in libsvm format
genome_to_libsvm	Converts a genome to kmers stored in libsvm format on disk
get_mic	Get MIC meta-data from feature database
kmers	Generates genome kmers
load_patric_db	Load PATRIC database
mic_censor	Censor MIC values
mic_range	Generate dilution series
mic_r_breakpoint	R breakpoint for MIC
mic_s_breakpoint	S breakpoint for MIC
mic_uncensor	Uncensor MICs
move_files	Move or copy files using logical vector
plot.mic_validation	Plot MIC validation results
print.mic_validation	Print MIC validation object
print.mic_validation_summary	Print MIC validation summary
pull_PATRIC_genomes	Automated download of genomes from PATRIC database
qc_in_range	Check that MIC is within QC range
qc_on_target	Check that QC measurement is at the required target *[Experimental]*
replace_multiple_slashes	Removes multiple slashes in a path or url
reverse_complement	Reverse complement of DNA string
split_and_combine_files	Create test train files from a number of files
squeezed_index_to_str	Get str conversion of squeezed kmer using index
squeezed_mers	Generates all permutations of squeezed kmers
standardise_mic	Standardise MIC to control strain *[Experimental]*
summary.mic_validation	Summary of MIC validation results
table	Table
table.default	Table
table.mic_validation	Table
tidy_patric_meta_data	Tidy PATRIC data
train_test_filesystem	Organise files into a train-test filesystem
unsqueezed_index_to_str	Get str conversion of unsqueezed kmer using index
unsqueezed_mers	Generates all permutations of unsqueezed kmers
xgb.cv.lowmem	Low memory cross-validation wrapper for XGBoost